From 1f46499e3b343de151fec3f31104b6c565e60179 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Tue, 21 Jan 2020 11:24:32 +0100
Subject: [PATCH] add bwa index

---
 tools/bwa/index/main.nf              | 16 ++++++++++++++++
 tools/bwa/index/meta.yml             | 25 +++++++++++++++++++++++++
 tools/bwa/index/test/main.nf         | 16 ++++++++++++++++
 tools/bwa/index/test/nextflow.config |  2 ++
 4 files changed, 59 insertions(+)
 create mode 100644 tools/bwa/index/main.nf
 create mode 100644 tools/bwa/index/meta.yml
 create mode 100644 tools/bwa/index/test/main.nf
 create mode 100644 tools/bwa/index/test/nextflow.config

diff --git a/tools/bwa/index/main.nf b/tools/bwa/index/main.nf
new file mode 100644
index 00000000..0c943bb4
--- /dev/null
+++ b/tools/bwa/index/main.nf
@@ -0,0 +1,16 @@
+process bwa_index {
+    tag {fasta}
+
+    container 'quay.io/biocontainers/bwa:0.7.17--hed695b0_7'
+
+    input:
+        path(fasta)
+
+    output:
+        path("${fasta}.*")
+
+    script:
+    """
+    bwa index ${fasta}
+    """
+}
\ No newline at end of file
diff --git a/tools/bwa/index/meta.yml b/tools/bwa/index/meta.yml
new file mode 100644
index 00000000..4509d34d
--- /dev/null
+++ b/tools/bwa/index/meta.yml
@@ -0,0 +1,25 @@
+name: bwa index
+description: create indexes for BWA from a fasta file
+keywords:
+    - index
+tools:
+    - bwa:
+        description: |
+            BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.
+        homepage: http://bio-bwa.sourceforge.net/
+        documentation: hhttp://www.htslib.org/doc/samtools.html
+        arxiv: arXiv:1303.3997
+input:
+    -
+        - input:
+            type: file
+            description: Input fasta file
+            pattern: *.{fasta,fa}
+output:
+    -
+        - index:
+            type: file
+            description: bwa indexes file
+            pattern: *.{fasta,fa}.{amb,ann,bwt,pac,sa}
+authors:
+    - @maxulysse
\ No newline at end of file
diff --git a/tools/bwa/index/test/main.nf b/tools/bwa/index/test/main.nf
new file mode 100644
index 00000000..6acb4d61
--- /dev/null
+++ b/tools/bwa/index/test/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+nextflow.preview.dsl = 2
+include '../../../nf-core/module_testing/check_process_outputs.nf' params(params)
+include '../main.nf' params(params)
+
+// Define input channels
+input = '../../../test-datasets/tools/bwa/index/input/reference.fasta'
+Channel
+  .from(input)
+  .set { ch_input }
+
+// Run the workflow
+workflow {
+    fastqc(ch_input)
+    // .check_output()
+}
diff --git a/tools/bwa/index/test/nextflow.config b/tools/bwa/index/test/nextflow.config
new file mode 100644
index 00000000..c137a138
--- /dev/null
+++ b/tools/bwa/index/test/nextflow.config
@@ -0,0 +1,2 @@
+docker.enabled = true
+params.outdir = './results'